nucleic acids Flashcards
what are 3 experiments that gave evidence that DNA is genetic material?
Griffith experiment (mice and smooth/rough strains of streptocuccus pneumoniae)
Avery (out of purified DNA, RNA, protein, lipid and carbohydrate, only DNA from the heat killed strain could induce viruence on non virulent strain)
Herschey and chase (radioactively labelled phages to show DNA carries genetic information)
describe the structure of a DNA molecule
anti parallel strands form a double helix
sugar phosphate backbone
phosphodiester bonds run in 5’ to 3’ direction to give directinality
base pairs join complementary strands together by hrydrogen bonding
2 H bonds between AT nd 3 H bonds between CG
packaging is tightly coiled with help of histones to fit into the nucleus
DNA+histones = chromatin (interphase)
active genes are more loosely coiled than silent genes
what experiment was used to show that DNA replication is semi-conservative?
Meseleson-stahl experiement - growing e-coli in a medium containing heavy isotope nitrogen 15 and after many generations switching to light nitrogen 14, then measuring the density of DNA by density gradient centrifugation, separating DNA into strands
how does DNA replicate?
DNA helicase unzips strands by breaking H bonds between base pairs
leading strand:
RNA primer binds to 3’ end (made by DNA primase)
DNA polymerase binds to strand at primer and begins adding new base pairs in 5’ to 3’ direction
lagging strand:
binding multiple primer, each primer is only several basses apart. DNA polymerase adds DNA = okasaki fragmnets between the primers = fragments
exonuclease removes RNA primers and replaced by appropriate bases by DNA polymerase. DNA ligase joins the okasaki fragments together
what reduces error frequency in replication?
DNA polymerases editing function that removes incorrectly insterted bases
other enzymes check
methylated C in DNA can mutate to T?
5-methylcytosine (5Mc) is caused by post-synthetic modification of cytosine residues mainly in CpG doubles. it is a mutable site and can undergo spontaneous deamination to thymine
What are DNA repair proteins?
they repair damage in DNA before replication
Base excision repair proteins cut out damaged bases (specific to certain types of damage)
Nucleotide excision repair proteins are less specific and cut out sections of damaged DNA strand
in both cases DNA polymerase replaces DNA removed by copying the intact strand and DNA ligase seals the gap
how many nucleotides are there compared to genes
3x10^9 nucelotides
19,000-20,000 genes
the human genome is much bigger than might be expected to accomodate genes of known function why?
much DNA is noncoding introns
what is synteny?
long DNA sequences are present in the same order across sepcies
single nucleotide polymorphisms can be associated with disease risk
Can result in amino acid substitution or introduce a stop codon (nonsense mutation0 resulting in a truncated proteins
what types of single nucleotide mutations are there?
point mutation
insertion
deletion
what are VNTR?
variable number tandem repeats, multiple copies of short sequences, unique length and number of repeats in individuals
what are VNTRs used for and how?
paternaty and forensic testing. because VNTRs are unique they can be amplified by PCR and compared by electrophoresis
3 differences between DNA and RNA?
RNA has ribose whereas DNA has deoxyribose
RNA contains uracil whereas DNA has thymine instead
RNA is single stranded, DNA is double stranded (if doubles stranded RNA is detected alarm response is set off as may suggest a viral infection)
describe DNA transcription
RNA polymerase binds to a sequence of DNA called the promoter, found near the beginning of a gene. Each gene has its own promoter. Once bound, RNA polymerase separates the DNA strands, providing the single stranded template needed for transcription
The template strand acts a template for RNA polymerase, it reads one base at a time 5’ to 3’, building up a RNA molecule by CBP, this carries the same information as the coding strand but has Uracil instead of Thymine
Terminator sequences – stop codon signal RNA transcript completetion. Causing the release from RNA polymerase.
what is the TATA box and what does it do?
Different promoter elements in eukaryotes including the TATA box. Short run of T and A bases (lowest energy base-pairs so easiest to unwind) that vary slightly from gene to gene and is probably the best characterised promoter element. Transcription factors bind to promoter to initiate transcription by binding the RNA polymerase to the region of the gene where transcription begins. Some promoter elements are several kB away from transcription site but TAT box is very close
what is and what does the CpG islands do?
Stretches of DNA where there are multiple points at which C is followed by G, occurring upstream of many genes, they are unmethylated regions of the genome associated with 5’ end of many genes and appear to have promoter activity of housekeeping genes (essential for general cell function)
how is eukaryotic mRNA modified by capping?
5’ end contains free triphosphate group since it was the first incorporated nucleotide in the chain the capping process replaces the triphosphate group with another structure called the cap, added by guanyl transferase. This enzyme catalyses the reaction between the 5’ end of the RNA transcript and guanine triphosphate (GTP) molecule
how is eukaryotic mRNA modified by polyadenylation?
Transcription continues past the point where a polyadenylation sequence is present. The mRNA is cut near the polyA sequence and a polyA tail is added to 3’ end
what does polycistronic mean and what kind of mRNA can be polycistronic?
when mRNA can code for multiple proteins (multiple genes per transcript), in prokaryotic mRNA
what are introns
non coding regions of mRNA
how are introns removed?
by splicing at specific sites at the start and end of each intron which are recognised by the spliceosome
what can alternative splicing do?
can generate related proteins from a single gene.
can generate subtly different mRNAs in related tissues
some RNA molelcules do not…
code for protiens, instead function in the RNA silencing and post transcription regulation of gene expression
what is the start codon?
Met/ methionine/ M
AUG
stop codons?
UAG
UAA
UGA
Basic structure of tRNA
clover leaf structure
what is the role of aminoacyl tRNA synthetase?
amino acids are esterified onto tRNA before being incorporated into proteins (by aminoacyl RNA synthetases which esterify the correct AA onto correct tRNA). The anticodon recognises codon on mRNA is at the end of one loop
describe the role of aminoacykase tRNA synthetase
- Synthetase recognises AA and tRNA
- Synthetase links AA to correct tRNA = amino acyl tRNA
- Aminoacyl tRNA is now ready to bind to mRNA and enables AA to be incorporated into protein
process of translation in the ribosome
- Initiation begins at start codon (AUG)
- Initiator et tRNA caries methionine (differes from normal tRNA that caries methionine) in bacteria this is N-formyl methionine.
- The intiator met tRNA is recognised by eukaryotic intiation factors
- These initiation factors bind to the small subunit of the ribosome and travel along the mRNA until initiating AUG is encountered
differences between prokaryotic and eukaryotic ribosomes and antibiotics that target prokaryotic ribosomes
• Prokaryotic ribosomes are 70S whereas eukaryotic ribosomes are bigger being 80S various antibiotics target ribosomes so need to be careful that they don’t damage a patients mitochondria as eukaryotic and prokaryotic ribosomes are similar
import of proteins into the mitochondria
proteins synthesised in the cytosol but destined for the mitochondria possess N-terminal signal sequences that determine their transport into the mitochondria. They are unfolded by molecular chaperones, transported through the mitochondrial memebranes then refolded using other chaperones in the mitochondria
import of proteins into the ER
The syntheseised protein passes into the lumen of the ER through a special pore
Secretory proteins are often modified after translation
Some modifications are permanent while others are reversible
Acetylation involves addition of an acetyl (CH3CO) group to the N-terminal end. It protects proteins against degradation.
Glycosylation is important In the formation of glycoproteins and proteoglycans
Phosphorylation is a common modification which reversibly modifies the activity of many enzymes and intracellular signal transducing proteins
Kinases add phosphate groups to the hydroxyl groups of serine, threonine and tyrosine
Phosphatases remove these groups
• A knowledge of gene structure and function together with protein
define cancer
Group of diseases, disease of bodys own
It is caused by uncontrolled cell division of abnormal cells in a part of the body
Features of cancer include uncontrolled celldivision, change in morphology, dedifferentiation of cells and cell migration into adjacent or distant tissues and loss of contact inhibition
what are the stages of tumour development
Normal cells, hyperproliferative cell population, early adenoma, late adenoma, carcinoma
causes of cancer
carcinogens - agents that increase risk of cancer
inherited cancer syndromes (Li Fraumeni syndrome)
environmental causes
biological (virus)
chemical (cigarette smoke and heterolytic amines in cooked meat)
physical (UV, X rays and gamma rays)
what modification is common in secretory proteins but does not occur in eukaryotic mRNA?
glycolysation
when does separation of sister chromatids occur?
second mitotic division
what cells repair skeletal muscle fibres?
satellite cells
what are fragments from the lagging strand in DNA replication called?
okasaki fragments
